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    <p><h1>Executable Arguments and Outputs</h1></p>
    <p>This page is a summary of all of the binaries that are created after 
      <tt>'make; make install'</tt> is run in the 
      enzo code bundle.  They should be located in the <tt>bin/</tt> directory.  Links to the various 
      pages of the manual that describe a particular binary are also included.</p>


    <p><b><font size=+1>enzo</font></b></p>
    <p>This is the main simulation code executable.  See <a href="cosmo_run.html">this page</a>
      for more detailed information.  In addition to performing the actual simulations, the enzo
      binary performs projections and various kinds of extractions.  Enzo projections are described
      on <a href="analyze.html#2D%20projections">here</a> and extractions are described on
      <a href="analyze.html#Extractions">here</a>.  The projection output file is called 
      <tt>amr.project</tt> and the extraction file is called <tt>amr.grid</tt>.</p>
      
    <p>When an Enzo simulation is run, at every datastep several files are output.  There is
      an ascii file which has no extension (ie, if your output dumps are named
      RedshiftOutput then the first parameter file output will be RedshiftOutput0000).  This
      file contains all of the parameters that Enzo needs to be able to restart the simulation,
      such as cosmology information, redshift, information on box volume, and which physics modules
      are turned on.  Another file, which has the same root and the extension '.hierarchy', contains
      ascii information on all of the Enzo AMR grids, such as their positions, sizes, number of particles
      per grid, etc.  There are two files with extensions '.boundary' and '.boundary.hdf' which contain
      information on boundary conditions.  And then there will be at least one file with the extension
      '.gridNNNN', where NNNN is a number between 0 and 9999. For simulations with more than 10,000
      files, the numbering will have 5 digits and start from 10000.  These files are where all of the 
      simulation data is actually contained.</p>

<pre>
usage: enzo [options] &lt;param_file&gt;

   general options:
      -d                            display debug information
      -r                            restart
      -x                            extract
      -l &lt;level&gt;                    level of extract
      -p &lt;dimension&gt;                project to plane
      -m                            smooth projection
      -o                            output as particle data
      -h                            help
      -i                            information output
      -s &lt;dim0&gt; [&lt;dim1&gt; [&lt;dim2&gt;]]   start index region
      -e &lt;dim0&gt; [&lt;dim1&gt; [&lt;dim2&gt;]]   end index region
      -b &lt;dim0&gt; [&lt;dim1&gt; [&lt;dim2&gt;]]   begin coordinates
      -f &lt;dim0&gt; [&lt;dim1&gt; [&lt;dim2&gt;]]   finish coordinate region

   performance options:
      -P mode &lt;modeval&gt;             set jbPerf mode
      -P event &lt;eventname&gt;          set jbPerf event
      -P dir &lt;directory&gt;            set jbPerf directory
</pre>


    <p>&nbsp;</p>
    <p><b><font size=+1>inits</font></b></p>
    <p>This is the initial conditions generator.  See <a href="index-inits.html">this page</a>
      for more detailed information.  Initial conditions with a single initial grid or multiple
      nested grids can be created with this executable.  Output file names are user-specified, but
      in a standard cosmology simulation with a single initial grid
      there should be a file containing baryon density information, another containing baryon velocity
      information, and two more files containing particle position and velocity information.  Simulations
      with multiple grids will have a set of these files for each level, appended with numbers to make them
      unique.</p>
    
<pre>
usage: inits [options] param_file
   options are:
      -d(ebug)
      -s(ubgrid) param_file
</pre>
    
    <p>&nbsp;</p>
    <p><b><font size=+1>ring</font></b></p>
    <p><tt>ring</tt> must be run on the simulation particle position and velocity information
      before a simulation is executed when the parameter <tt>ParallelParticleIO</tt> is set to 1.
      Running ring generates files called PPos.nnnn PVel.nnnn  where nnnn goes from 0001 to the 
      total number of processors that are used for the simulation.  These files contain the particle
      position and velocity information for particles that belong to each processor individually,
      and will be read into the code instead of the monolithic particle position and velocity files.
      Note that if <tt>ParallelParticleIO</tt> is on and ring is NOT run, the simulation will crash.</p>


<pre>
usage:  ring &lt;particle position file&gt; &lt;particle velocity file&gt;
</pre>


    
    <p>&nbsp;</p>
    <p><b><font size=+1>differ</font></b></p>
    <p>This piece of code compares two different HDF5 files/datasets (which are supposedly the same) and
      tells how many values are different, and outputs this to stdout.  No files are output.</p>

<pre>
usage:  differ &lt;file 1&gt; &lt;file 2&gt; &lt;dataname 1&gt; &lt;dataname 2&gt;    
</pre>


    <p>&nbsp;</p>
    <p><b><font size=+1>glue</font></b></p>
    <p>Glue takes single-grid or fractured unigrid enzo hierarchies (ie, ones that have been created using 
      a simulation with <tt>ParallelRootGridIO</tt> on) and extracts individual fields into monolithic
      files, which is useful for user-written data analysis.  The files that are output have the same
      name as the field name.</p>

<pre>
usage:  glue &lt;GridName&gt; &lt;FieldName&gt; &lt;gridsize&gt; &lt;ngrids&gt;
</pre>


    <p>&nbsp;</p>
    <p><b><font size=+1>dumpgrids</font></b></p>
    <p>This executable takes an enzo hierarchy (amr or unigrid) and outputs all non-overlapping
      cells into a file called DumpGridData.grid in four column format, corresponding to:
      temperature, density, (junk), grid size, all of which are in code units.</p>

<pre>
usage: dumpgrids [-d] [-g] [-p] [-s] amr_saved_filename [dump_filename]
  -d)ebug
  -g)rid data output
  -p)article data output
  -s)tar data output
</pre>

    <p>&nbsp;</p>
    <p><b><font size=+1>enzo_anyl</font></b></p>
    <p>This executable generates sperhically-averaged radial profiles of halos.  
      See <a href="analyze.html#profiler">this page</a> for more information. <tt>enzo_anyl</tt>
      dumps information into files that start with the string 'AnalyzeCluster'.  See the previously
      mentioned page for more details.</a>

<pre>
usage: enzo_anyl amr_file anyl_parameter_file
</pre>


    <p>&nbsp;</p>
    <p><b><font size=+1>enzostats</font></b></p>
    <p>This code generates some globally averaged information about a given simulation.  No files
      are output, only information to stdout.</p>
<pre>
    enzostats [-b #] [-f #] [-d] amr_file
  -b)egin region
  -f)inish region
  -d)ebug
</pre>



    <p>&nbsp;</p>
    <p><b><font size=+1>findinit</font></b></p>
    <p>This binary finds the extent of the initial positions of all particles in a given halo.  It
      is used for generating multi-grid initial conditions, and more information about it can be
      found <a href="index-inits.html#multigrid">here</a>.  No files are input, only text to
      stdout.</p>

<pre>
    usage: findinit amr_final_output amr_initial_output cluster_file
    or: findinit amr_output cluster_file
    (cluster_file format: x y z r   in box units)
</pre>
    <p>&nbsp;</p>
    <p><b><font size=+1>findpeaks</font></b></p>
    <p>One of the two methods for finding density peaks (ie, halos) in an Enzo simulation.  
      More information can be found <a href="analyze.html#Peakfinder">here</a>.  The output
      is an ascii file with a user-specified filename (cluster_file) where there are halo
      positions sorted by peak density.</p>

<pre>    
usage: findpeaks [options] amr_file cluster_file
  options: -n # (number of peaks)
           -m # (minimum density)
           -s # (min peak separation, comoving Mpc)
           -b   (use baryon density in peak seach, default)
           -d   (use dark matter density in peak seach)
           -p   (use potential in peak search)
           -x   (use bolometric x-ray in peak seach)
</pre>


    <p>&nbsp;</p>
    <p><b><font size=+1>enzohop</font></b></p>
    <p>The second (and generally favored) method used for finding density peaks in an Enzo simulation.
      More information can be found <a href="analyze.html#halofinder">here</a>.  A file called
      HopAnalysis.out is output which contains halo position and mass information.</p>

<pre>
enzohop [-b #] [-f #] [-t #] [-g] [-d] amr_file
  -b)egin region
  -f)inish region
  -t)hreshold for hop (default 160)
  -g)as particles also used (normally just dm)
  -d)ebug
</pre>



<p>&nbsp;</p>
<p>&nbsp;</p>
<p>
<a href="../index.html">Go to the Enzo home page</a>
</p>

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<center>&copy; 2004 &nbsp; <a href="http://cosmos.ucsd.edu">Laboratory for Computational Astrophysics</a><br></center>
    <center>last modified February 2004<br>
      by <a href="mailto:bwoshea (AT) lanl.gov">B.W. O'Shea</a></center>
    
    
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